Diel activity structures occurrence of mammal community in human dominated landscape

Data and R code for fitting multi-stated diel occupancy models to 14 species sampled in Rhode Island, USA.

In the "Data" subfolder are each species' detection matrices saved as R objects, e.g., 'bobcat.MSDOM.RI.Data' . Each object is a list of two elements. The first element is a detection matrix that has sites on the rows and occasions on the columns. The second element is a matrix of site-level covariates. The sub-sub folder 'covariates' has covariate values in csv and xlsx files; note that the covariates used for model fitting are in the R data objects. 

In the 'Models' subfolder are four R files specifying the JAGS models used to fit the data. Each model specifies the full or reduced model parameterizations of the multi-sate occupancy model with or without covariates. 

The subfolder 'Outputs' is the folder that MCMC and summary files are exported from the R scripts.

In the subfolder 'scripts' are R scripts to fit multi-state diel occupancy models (files: Base.Model.fit.each.species.r, Covariate.Model.fit.each.species.with.DetectionSimple.r, and Covariate.Model.fit.each.species.with.DetectionSimple.REDUCED.r) and calculate CPO used for model selection (files: CPO.function.r, extract.p.r, multi.state.likelihood.r).